Ayr - Micklefield SOR (Route Appleby ) is £52.80
Ayr - Leeds Route SOR (Route Dumfries & Appleby) is £45.40
Saltaire-York SVR (valid any train) is £14.30
You are
doubly valid between Saltaire and Micklefield (or 'only' between Shipley and Leeds unless you're on stoppers).
Yes it's cheaper to be doubly valid for part of your journey with split tickets, than to get one ticket. Crazy, but true, and no I am not surprised.
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Further edit: if the Dumfries and Appleby route appeals, then Ayr to Settle via Dumfries is £37.70 SOR and Settle to York is £22.00 SOR - total of £59.70.
I can't beat that price, I can only beat it on the basis of having 2 valid tickets for about 35 miles at the same price of £59.70
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OK I've got it.
Prestwick Atrain - Carlisle SVR £8.80 (Route Dumfries)
Then a Freedom of the North East 4 in 8 at £75.00
This is 80p more than the through via Dumfries fare, and for 80p you get unlimited travel for 4 days in the area

You can also go via Newcastle or Appleby, and down to Sheffield if you want!
Or..
Prestwick Atrain - Carlisle SVR £8.80 (Route Dumfries)
Carlisle-York SOR £39.30 SOR (Route Appleby)
Total = £48.10
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Would a Ayr-Berwick-on-Tweed ticket be valid via York?
If so, the SVR is valid at any time and costs £43.00.
Only if they've made an error on the scale of that Slough to Reading (or whatever it was!) via Exeter
